Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
colon
chip antibody
cat no:33-9900, lot no: QJ216251, mouse monoclonal, Invitrogen
cell line
SW480
transfection
stably transfected with empty vector

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with DSG (20593, lot TF263080, Thermo Scientific) for 45 min and then incubated with formaldehyde (1%) for 10 minutes. Nuclear chormatin fractions were separted and immunoprecipitated with P65 anitboides. The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

Sequencing Platform

instrument_model
NextSeq 550

hg38

Number of total reads
52122209
Reads aligned (%)
88.7
Duplicates removed (%)
2.8
Number of peaks
1616 (qval < 1E-05)

hg19

Number of total reads
52122209
Reads aligned (%)
88.1
Duplicates removed (%)
3.8
Number of peaks
1692 (qval < 1E-05)

Base call quality data from DBCLS SRA